def _next(self, line):
if len(line)>0 and line[0]=='#':
return None
origCols = line.split('\t')
cols = [unquote(x) for x in origCols]
if len(cols) != 9:
raise InvalidFormatError("Error: GFF files must contain 9 tab-separated columns")
ge = GenomeElement(self._genome)
ge.chr = self._checkValidChr(cols[0])
ge.source = cols[1]
ge.type = cols[2]
ge.start = self._checkValidStart(ge.chr, int(cols[3]) - 1)
ge.end = self._checkValidEnd(ge.chr, int(cols[4]), start=ge.start)
ge.val = numpy.float(self._handleNan(cols[5]))
ge.strand = self._getStrandFromString(cols[6])
ge.phase = cols[7]
ge.attributes = cols[8]
for attr in origCols[8].split(';'):
attrSplitted = attr.split('=')
if len(attrSplitted) == 2:
key, val = attrSplitted
if key.lower() == 'id':
ge.id = unquote(val)
elif key.lower() == 'name':
ge.name = unquote(val)
return ge
def _next(self, line):
cols = line.split('\t')
ge = GenomeElement(self._genome)
ge.chr = self._checkValidChr(cols[0])
ge.start = int(cols[1])
ge.end = int(cols[2])
self._parseVal(ge, cols[3])
return ge
def _next(self, line):
cols = line.split('\t')
ge = GenomeElement(self._genome)
ge.chr = self._checkValidChr(cols[0])
ge.start = int(cols[1])
ge.end = int(cols[2])
self._parseVal(ge, cols[3])
return ge
def _next(self, line):
if line.startswith('##FASTA'):
raise StopIteration
if len(line) > 0 and line[0] == '#':
return None
origCols = line.split('\t')
cols = [unquote(x) for x in origCols]
if len(cols) != 9:
raise InvalidFormatError(
"Error: GFF files must contain 9 tab-separated columns")
ge = GenomeElement(self._genome)
ge.chr = self._checkValidChr(cols[0])
ge.source = cols[1]
self._parseThirdCol(ge, cols[2])
ge.start = self._checkValidStart(ge.chr, int(cols[3]) - 1)
ge.end = self._checkValidEnd(ge.chr, int(cols[4]), start=ge.start)
self._parseSixthCol(ge, cols[5])
ge.strand = self._getStrandFromString(cols[6])
ge.phase = cols[7]
ge.attributes = cols[8]
for attr in origCols[8].split(';'):
attrSplitted = attr.split('=')
if len(attrSplitted) == 2:
key, val = attrSplitted
if key.lower() == 'id':
ge.id = unquote(val)
elif key.lower() == 'name':
ge.name = unquote(val)
return ge